Cancer is a major cause of human death worldwide. The vast majority of cancer patients suffer from solid tumors whose growth destroys vital organs. We propose to develop novel therapeutic drugs that target solid tumors affecting the brain, colon and ovaries. These cancers account for a significant proportion of currently intractable solid malignancies.
Scientists have made great strides in understanding the molecular and cellular changes that cause cancer but the approval of new therapeutics that can specifically kill cancer cells has lagged behind. This disparity suggests that there must be critical bottlenecks impeding the process of turning a basic research discovery into a finished anti-cancer drug. Research over the past decade has given rise to the idea that one of these bottlenecks may be caused by the existence of cancer stem cells. According to the cancer stem cell hypothesis, there is a minor population of cancer stem cells that drives the growth of the entire tumor. However, cancer stem cells are very rare and hard to identify. Technical innovations have recently allowed the identification, isolation and growth of these cells in the laboratory, and it has become clear that they have properties that are distinct from both the bulk of tumor cells and the cancer cell lines usually used to test anticancer drug candidates. Furthermore, in the lab, cancer stem cells are resistant to the chemotherapy and radiation treatments used to kill most tumor cells. In a patient, cancer stem cells may not be killed by standard drugs and may eventually regrow the tumor, causing a cancer to relapse or spread. Thus, a drug that specifically targets cancer stem cells could dramatically improve the chances of treatment success.
Our team is one of the few in the world that can identify cancer stem cells in brain, colon and ovarian tumors. Furthermore, we have developed assays that can accurately test the effectiveness of drug candidates in killing these cells. Our preliminary data suggest that our lead drug candidates can inhibit the growth of cancer stem cells in culture and block tumor initiation in animal models. Importantly, our drug candidates appear to work through mechanisms that are different from those employed by current chemotherapeutics, meaning that our drugs represent a fresh and potentially very effective approach to cancer treatment. Over the next several years, we propose to complete our development and preclinical studies of these drugs so that testing in cancer patients can begin.

Statement of Benefit to California:

Our proposal may benefit the state of California in four important ways. First, solid tumors cause significant morbidity and mortality. We propose to develop 2-3 Investigational New Drugs (INDs) to treat colon, brain and ovarian tumors, which are often difficult to treat with conventional therapies and are associated with poor prognoses. Thus, the proposed INDs should lead to a decreased burden on the California health system.
The second benefit arises from our novel approach to drug development, a route that other researchers may emulate. Most targeted cancer drugs fail in clinical trials, despite our growing knowledge of the molecular and cellular causes of cancer. These failures indicate that there are rate-limiting factors in the way basic research is currently translated to cancer drug discovery and development. One such factor may be related to a major new hypothesis in tumorigenesis, which states that a minor population of cancer initiating cells (CICs) drives bulk tumor growth. These CICs appear to survive existing therapies that kill most tumor cells, and so can go on to initiate relapses and metastases. A second rate-limiting factor may be the heterogeneity that exists both among and within different tumor types. Both of these “bottleneck” factors can be obviated by the molecular characterization and comparison of CICs and bulk tumor cells. Knowing the features that distinguish CICs from bulk tumor cells will facilitate a targeted drug development plan that optimizes chances for clinical success. We have devised such a strategy based on the integration of solutions to these limiting factors into a state-of-the-art drug discovery platform. This strategy may provide a foundation for the rapid extension of our approach to the treatment of other solid tumors.
The third benefit is the linking of CIC identification to clinical outcome. The ability to isolate and propagate CICs from solid tumors is a recent innovation. We will perform a thorough genetic examination of the alterations in these cells that lead to oncogenesis. Because we intend to carry out this work in parallel with the characterization of tumor samples from patients with documented clinical outcomes, we will be able to correlate the nature of particular CICs with similarities/differences among human tumors in a way that identifies features statistically linked to poor outcomes. This information will allow the selection and validation of additional drugs so that a pipeline of ever more refined compounds is established even if initial attempts fail in the clinic.
The fourth benefit falls directly in line with the focus of California’s robust biotechnology industry on drugs to address unmet medical needs. Our data and methods will be published and readily available, and so can be applied by existing and emerging biotech companies. Great advances in novel targeted therapeutics to treat solid tumors should be realized, expanding the drug development expertise of the state.

Progress Report:

Year 1

The objective of our collaborative project is the development of therapeutic candidates that will form the basis of IND submissions designed to test a novel class of drugs for the treatment of tumor initiating cells (TICs) in three solid human malignancies where TICs have been implicated in the pathogenesis of disease. The target profile is the TIC population in colon cancer, ovarian cancer and glioblastoma. The therapeutic compounds that have been developed in the course of the collaboration target a pair of serine-threonine kinases that act at the nexus of mitosis, hypoxia, and DNA repair. These enzymes are over-expressed in many forms of cancer and alterations in their expression patterns correlate with dysregulation of a number of genes that are significantly linked to poor patient outcome.
Compounds against the first target have been developed to the point at which a developmental candidate can be selected. The compounds show single digit nanomolar potency in vitro, adequate specificity, appropriate pharmacokinetics to support oral delivery, and the ability to trigger growth inhibition and cell death in a wide panel of tumor cell lines and TICs from the three targeted histologies. Recently completed dose and schedule studies have been used to design and implement tumor model studies. The compound that demonstrates the widest therapeutic index will be selected for IND enabling studies. These IND enabling studies will include synthetic scale-up, toxicity evaluations, combination studies, mechanism of action studies, and a biomarker identification program that will be used to identify a targeted population for optimal clinical trial design.
The medicinal chemistry program against the second target was started approximately 15 months after the initiation of the effort against the first target. Sufficient potency, specificity, and activity against tumor cell lines and TICs have been demonstrated with novel molecules. Current efforts are focused on improving the pharmacokinetic properties of the drug candidates.
A phospho-flow platform to measure mRNA levels, protein levels, and enzymatic activity using a mass spectrometric readout has also been tested. This system enables the simultaneous measurement of up to 35 different biomolecules. A data management system has been developed to facilitate the associated complex data analysis. Proof or principle experiments have demonstrated that this experimental paradigm can be used to reconstruct the developmental lineages of all progeny downstream of hematopoietic stem cells from human and mouse bone marrow. This approach has recently been applied to the analysis of ovarian cancer cells taken directly from patients. The results of these studies suggest that cancer cells are clearly heterogenous, but perhaps most importantly can be organized into developmental lineages that are formally similar to those seen in bone marrow development. Furthermore, this platform can assess the response of individual subcomponents of the oncological lineage to both approved and experimental drugs. We will be using this platform to gain insight into how tumors respond to individual drugs, including our drug candidates, and combination studies. It is reasonable to expect that it will be possible to not only assess the response of the cancer stem cells, but all subtypes of the tumor lineage.

Year 2

Slamon Mak Cancer Stem Cell Abstract
Drug discovery programs against two different mitotic kinases are being pursued. Both programs follow the same general process flow in which lead optimization experiments culminate in the selection of a single small molecule candidate for advancement to preclinical development. The development candidate then proceeds through a standard series of evaluations to establish its suitability for an IND submission and use in subsequent clinical trials.
CFI-003 was selected as a clinical development candidate and is progressing through investigational new drug application (IND)-enabling studies. Chemistry activity in the past year has included the selection of the fumarate salt as the final salt form, and production of two kilogram-scale clinical batches, the first of which is scheduled to be released at the end of April. The compound is stable when stored under typical storage conditions, and has an impurity profile that is safe for clinical dosing. In cancer models, CFI-003 was shown to be particularly effective against tumors deficient for the tumor suppressor gene PTEN; this is important given that deficiencies in this gene are generally considered to be an indicator of poor prognosis in the clinic. Experiments are ongoing to determine biomarkers of response to CFI-003 for application in the clinic. Other work includes selection and management of contract research organizations (CROs) for critical IND-enabling studies. For example, Pharmatek has been engaged to assist in the development of a drug formulation that enhances the stability of CFI-003, and maximizes bioavailability of the compound when dosed orally. Other CRO work that is ongoing involves in vitro pharmacology experiments geared toward understanding how CFI-003 might interact with co-administered drugs, and performing key toxicology experiments for determination of a safe and effective clinical dose of the compound. An important milestone was reached in the previous reporting period in that the patent application covering CFI-003 was allowed by the US patent office. The CFI-003 IND development team will continue to move the project forward planning for a successful IND submission toward the end of Q1 2013.
The drug discovery efforts in the second program have been focused on improving the pharmacokinetic properties of the lead series molecules while maintaining excellent in vitro activity. Approximately 400 new chemical entities have been synthesized during the last reporting period. Progress to date has been measured by an increase in potency in the biochemical assay and improved anti-proliferative potency in cancer cell growth assays. Activity toward Aurora B has simultaneously been attenuated, and current compounds demonstrate improved selectivity against a diverse panel of kinases. Progress was aided by the acquisition of multiple co-complex x-ray structures which allowed for further refinement of binding models to the target’s active site. Compounds to be qualified for further study must continue to induce an aneuploidy phenotype at least an order of magnitude above the HCT116 (colon adenocarcinoma cell line) GI50, and importantly must also demonstrate adequate plasma levels upon oral dosing. A lead series compound has been shown to have oral efficacy in a cancer model. To follow up this result, additional compounds have been scaled up for testing. Experiments to determine the tolerability have been completed for the latest candidates and further efficacy studies have been initiated. Results from these efficacy studies will aid in the identification of a development candidate for subsequent IND enabling studies.

Year 3

Drug discovery programs against two different mitotic kinases are being pursued. Both programs follow the same general process flow in which lead optimization experiments culminate in the selection of a single small molecule candidate for advancement to preclinical development. The development candidate then proceeds through a standard series of evaluations to establish its suitability for an IND submission and use in subsequent clinical trials.
CFI-400945 was selected as a clinical development candidate. The IND-enabling studies included the selection of the fumarate salt as the final salt form, and the production of two kilogram-scale clinical batches, which have been released during the past year. The compound is stable when stored under typical storage conditions, and has an impurity profile that is safe for clinical dosing. In cancer models in mice, CFI-400945 was shown to be particularly effective against specific subsets of tumor cell lines in both tumor cells grown in soft agar and in xenograft models. Experiments are ongoing to determine biomarkers of response to CFI-400945 for application in the clinic. Pharmatek was engaged to assist in the development of a drug formulation that enhanced the stability of CFI-400945, and maximized the bioavailability of the compound when dosed orally. Other CRO work that was completed included in vitro pharmacology experiments geared toward understanding how CFI-400945 might interact with co-administered drugs, and performing key toxicology experiments in animals for determination of a safe and effective clinical dose of the compound. This work culminated in an IND submission in the second quarter of 2013.
The drug discovery efforts in the second program has focused on improving the pharmacokinetic properties of the lead series molecules while maintaining excellent in vitro activity. Approximately 400 new chemical entities were synthesized and tested using a battery of biochemical and cell-based assays. Off target activity towards Aurora B has simultaneously been attenuated, and current compounds demonstrate improved selectivity against a diverse panel of kinases. Progress was aided by the acquisition of multiple co-complex x-ray structures which allowed for further refinement of binding models to the target’s active site. Compounds were qualified for in vivo study based on the induction of an aneuploid phenotype at an order of magnitude above the HCT116 (colon adenocarcinoma cell line) GI50, and importantly the demonstration high mouse plasma levels upon oral dosing. Mouse xenograft studies based on a number of tumor cell lines were used to select a short list of compounds. The aggregate data was then used to select a developmental candidate CFI-1870. IND enabling studies have been launched. In parallel, detailed dose and schedule studies are underway along with approaches to identify susceptible tumor subpopulations and associated biomarkers that will eventually support a targeted clinical trial.

Year 4

The Slamon/Mak cancer stem cell drug discovery program funded by CIRM/CSCC has achieved two important milestones in the past year. Our first therapeutic candidate was approved by the FDA and first-in-human dosing of CFI-400945 has taken place as part of the Phase I clinical trial. In our second program we have selected a development candidate that is now in the midst of IND ennabling studies
The clinical trial is being carried out at Princess Margaret Cancer Centre (Principal Investigator, Dr Philippe Bedard) and UCLA (Principal Investigator, Dr Zev Wainberg). This clinical trial was initiated after a number of milestones were successfully met following the submission of the IND and CTA in 2013. These have included making improvements to the formulation of the CFI-400945 tablets resulting in the successful reduction of the appearance of a degradant that was slowly accumulating in the initial formulation. This enabled the manufacturing of the cGMP tablets for use in the clinic in September 2013. These formulation changes and the Certificates of Analysis of these tablets were submitted to the FDA and permission was granted to begin clinical evaluation. In December 2013, we were awarded the CIRM Disease Team III funding to continue the CFI-400945 program which enabled the planning and initiation of this Phase I clinical evaluation and additional non-clinical studies.
In our second program, Pyrazolo-pyrimidines have emerged as the most promising class of 3rd series TTK inhibitors. TTKis with potent in vitro activity, excellent oral exposure in rats and in vivo efficacy were identified. A short list of 5 pyrazolo-pyrimidines was identified as potential third series development candidates. After further characterization it was determined that 4 or 5 compounds met the preponderance of the selection criteria, 2 of which had outstanding PK properties. The TTK inhibitor CFI-402257 had the best balance of efficacy, PK and off-target activities and was selected as the development candidate. IND enabling studies with 402257 have been initiated, and will continue during the no cost extension period of the grant.